In our recent transcriptomic analysis of T. gondii, we used UMAP and HDBSCAN clustering to examine the organism's transcriptional landscape through its developmental stages. Initially, a low variance threshold led to many genes being labeled as noise and unclear clusters with low silhouette scores. To improve clarity, we set a stricter variance threshold of 2, reducing our dataset to 4,883 genes and enhancing the identification of distinct transcriptional signatures.

This UMAP graph displays the outcomes of stringent variance-based filtering on T. gondii bulk RNA-seq data from the Hehl Lab. By setting the threshold to the mean plus standard deviation of gene variances, we narrowed the dataset down to 935 genes. The resulting analysis identified five distinct clusters with no overlapping or noise, offering clear insights into the transcriptional profiles of the organism.